1) Are you using the latest beta version of adxv? 2) Load the adx file (yes it is an ASCII text file...one for every diffraction image in your working directory) and load also the diffraction image. I also saw the white background after loading the adx file, but after loading the image I got the predictions in blue squares. If the predictions still do not show up, go to view-> predictions and click on the box that says 'show predictions'.
If you have generated the adx files then your generate_adx is ok. Still I am attaching the fortran code ... just in case you wanna try that. El mar, 20 de jul. de 2021 a la(s) 15:56, Doo Nam Kim (doonam....@pnnl.gov) escribió: > Hello Murpholino, > > Thank you for your comment and nice screenshot. > > Can you send me your Fortran code that you used to compile by gfortran as > a text file? > That is what I need. > > Unfortunately, I can't run your generate_adx binary with > ./generate_adx: error while loading shared libraries: libgfortran.so.5: > cannot open shared object file: No such file or directory > > So I need to compile by myself. > > However, whenever I copied code from > https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_adx > directly, compiled binary either results in *.a file or file without any > extension. > > Even when I manually modified/added extension as .adx, my adxv doesn't > show any real image (nothing but white background like attached). > although these result files have numerical values > (e.g. > 1091 24 10 24 6 > 505 361 10 3 22 > 616 296 10 7 19 > 865 58 11 18 13 > ...) > (as a note, my adxv is loading other .mrcs files well). > > I assume that whenever I copied code from > https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_adx > some trailing whitespace/carriage returns are copied as well invisibly. > > Sincerely, > Doo Nam > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
! Task: generate .adx files from existing XDS.INP and XDS_ASCII.HKL ! to be able to visualize where XDS finds/expects reflections ! The latest beta versions of ADXV (from http://www.scripps.edu/~arvai/adxv/) ! can read these .adx files and display them together with the frames. ! Compilation: save this code as "generate_adx.f90" and compile with e.g. ! gfortran -O -C generate_adx.f90 -o generate_adx ! Then move the resulting binary to /usr/local/bin or ~/bin ! Usage: go to the directory which has XDS_ASCII.HKL and run generate_adx ! ! Kay Diederichs 6/2009 ! implicit none integer :: hkl(3),iframe,j=-10000,mini=huge(mini),maxi=-huge(maxi),& nref=0,i,i1,i2,num real intensity,sigi,x,y,z character :: string*132,frmnam*103,form*6='(i0.0)' logical :: back=.true. 100 format(5i5) 101 format(a) ! find out NAME_TEMPLATE_OF_DATA_FRAMES open(1,file='XDS.INP',status='old') do read(1,101,end=98) string string=adjustl(string) if (string(:29)=='NAME_TEMPLATE_OF_DATA_FRAMES=') then frmnam=adjustl(string(30:)) i1=index(frmnam,'!') if (i1>0) frmnam=frmnam(:i1-1) if (index(frmnam,'.',back)>index(frmnam,'?',back)) then frmnam=frmnam(:index(frmnam,'.',back))//'adx' ! exchange extension else frmnam=frmnam(:len_trim(frmnam))//'.adx' ! add extension endif endif end do 98 close(1) print*,'.adx names :',frmnam(:len_trim(frmnam)) ! prepare modification of framename i1=index(frmnam,'?') i2=0 do i=i1,len_trim(frmnam) if (frmnam(i:i)=='?') then i2=i else exit endif end do if (i2==0) stop 'template should contain a ?' write(form(3:3),'(i1)') i2-i1+1 form(5:5)=form(3:3) ! sort XDS_ASCII.HKL by frame number print*,'sorting XDS_ASCII.HKL ...' call system('grep -v \! XDS_ASCII.HKL | sort -k 8n > temp_adx.sort') open(1,file='temp_adx.sort') print*,'sorting XDS_ASCII.HKL done' num=10000 do read(1,*,end=99)hkl,intensity,sigi,x,y,z iframe=int(z)+1 mini=min(iframe,mini) maxi=max(iframe,maxi) nref=nref+1 if (mod(nref,num)==0) then print*,'working',num num=num*2 endif if (iframe/=j) then ! new frame write(frmnam(i1:i2),form) iframe if (j/=-10000) close(2) open(2,file=frmnam) j=iframe endif ! XDS starts counting at 1, whereas ADXV starts at 0: write(string,100) nint(x)-1,nint(y)-1,hkl call removeblanks(string) write(2,101)string(:len_trim(string)) end do 99 print*,'first frame, last frame, nref=',mini,maxi,nref close(1,status='delete') close(2) end ! subroutine removeblanks(string) ! Removes leading and trailing blanks, and turns multiple blanks into one blank. implicit none character string*(*),copy*132 integer i,j logical first j=0 first=.false. do i=1,len_trim(string) if (string(i:i) /= ' ') then j=j+1 copy(j:j)=string(i:i) first=.true. elseif (first) then j=j+1 copy(j:j)=string(i:i) first=.false. endif end do string=copy(1:j) end
